Re: [PyMOL] exporting maps

[Thomas H. <tho...@sc...>]

Hi Daniel,

PyMOL 1.7.4 has a Python API function to access a map as a numpy array: cmd.get_volume_field, it takes the name of a map or volume object as its first argument. PyMOL doesn't support any map formal for export, but with this function you could write your own routine.

Example:

cmd.fetch("1ubq")
cmd.map_new("pseudomap")
data = cmd.get_volume_field("pseudomap")

# grid size
print data.shape

# world-space dimensions
print cmd.get_extent("pseudomap")

# raw data
print data

Hope that helps.

Cheers,
  Thomas

On 09 Jan 2015, at 04:19, Daniel Larsson <la...@xr...> wrote:

> I have created a pseudo-low resolution electron density map from a PDB-file using the map_new command. Is it possible to export or save that map to a file? Any format should be fine.
> 
> Daniel

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.